Contacts of the helix formed by residues 154 - 172 (chain P) in PDB entry 2D2I
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 154 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P PRO* 3.6 23.2 - - - +
153P ALA* 1.3 77.0 - - - +
155P CYS* 1.3 67.4 + - - +
156P THR* 3.5 3.9 + - - -
157P THR* 3.2 22.9 + - - -
158P ASN* 3.0 26.9 + - - +
322P TYR* 3.6 4.0 - - - -
4339P SO4 3.0 34.8 + - - -
4341P NAP 5.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 155 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P SER* 1.3 77.3 - - - +
156P THR* 1.3 72.6 + - - +
158P ASN* 3.2 12.1 + - - +
159P CYS 3.3 7.6 + - - -
182P HIS* 3.5 28.7 - - - -
294P SER 5.1 0.3 - - - +
316P TYR* 3.6 12.9 - - + -
318P ASN* 3.6 31.4 - - + +
322P TYR* 3.5 17.6 - - + -
4339P SO4 5.2 3.1 - - - -
4340P SO4 5.5 3.1 - - - -
4341P NAP 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P SER* 3.3 3.7 + - - -
155P CYS* 1.3 79.7 - - - +
157P THR* 1.3 58.0 + - - +
159P CYS* 2.9 4.9 + - - +
160P LEU* 2.8 28.4 + - + +
178P MET* 4.3 8.7 - - - -
180P THR* 3.9 15.7 + - + +
182P HIS* 3.7 13.9 + - - -
215P ALA* 3.4 25.1 - - + -
245P VAL* 3.9 15.3 - - + -
316P TYR* 2.9 27.4 + - - +
4339P SO4 3.7 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P THR* 6.3 0.2 - - + -
134P VAL* 4.3 9.6 - - + -
153P ALA* 3.9 20.9 - - + -
154P SER* 3.2 16.5 + - - -
156P THR* 1.3 79.0 - - - +
158P ASN* 1.3 58.1 + - - +
160P LEU* 4.2 6.1 - - - -
161P ALA* 2.9 36.3 + - + +
215P ALA* 3.1 35.0 + - - +
218P ALA* 3.6 16.2 - - + +
219P VAL* 4.4 10.1 - - + +
222P VAL* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 158 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P VAL* 3.7 25.7 - - - +
135P ILE 4.5 0.6 - - - +
152P ASN* 2.7 39.7 - - - +
153P ALA* 4.0 1.6 - - - +
154P SER 3.0 18.2 + - - +
155P CYS* 3.6 11.0 - - - +
156P THR 3.1 0.4 - - - -
157P THR* 1.3 78.0 - - - +
159P CYS* 1.3 58.0 - - - +
162P PRO* 3.0 18.3 - - - +
294P SER* 3.1 24.6 + - - +
322P TYR* 3.7 14.2 - - + -
325P ARG* 3.7 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 159 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155P CYS 3.3 4.4 + - - +
156P THR 2.9 7.9 + - - +
158P ASN* 1.3 77.3 - - - +
160P LEU* 1.3 66.2 + - - +
162P PRO* 3.6 2.4 - - - +
163P VAL* 3.6 8.5 - - - +
245P VAL* 3.2 30.5 - - + -
294P SER 3.3 15.9 + - - +
295P SER* 3.1 37.9 + - - -
314P ALA* 3.5 14.8 - - - -
316P TYR* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156P THR* 2.8 16.5 + - + +
157P THR* 3.9 3.6 - - - +
159P CYS* 1.3 79.1 - - - +
161P ALA* 1.3 66.2 + - - +
163P VAL* 3.1 8.3 + - + +
164P ALA* 2.8 26.4 + - + +
178P MET* 3.9 30.1 - - + -
215P ALA* 4.0 7.2 - - + +
216P ALA* 3.9 14.8 - - - +
219P VAL* 3.6 25.8 - - + -
230P LEU* 4.9 6.3 - - + -
245P VAL* 4.9 10.5 - - + +
247P LEU* 3.8 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P VAL* 4.2 4.9 - - + -
137P VAL* 4.1 9.6 - - + -
157P THR* 2.9 26.8 + - + +
160P LEU* 1.3 74.3 - - - +
162P PRO* 1.3 62.3 - - + +
164P ALA* 3.2 5.8 + - - -
165P LYS* 2.8 32.2 + - - +
219P VAL* 4.3 11.2 - - + +
222P VAL* 4.0 27.1 - - + -
223P ILE* 3.6 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 162 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P VAL* 4.4 4.5 - - + -
137P VAL* 4.1 13.2 - - + -
158P ASN* 3.0 29.4 - - - +
159P CYS 3.6 6.7 - - - +
161P ALA* 1.3 91.9 - - + +
163P VAL* 1.3 60.5 + - - +
165P LYS 3.4 0.2 + - - -
166P VAL* 3.2 21.0 + - - +
272P MET* 3.5 31.4 - - + +
275P ILE* 3.6 26.5 - - + -
276P ILE* 3.8 12.8 - - + -
294P SER* 4.6 0.4 - - - -
295P SER* 4.0 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159P CYS 3.6 15.7 - - - +
160P LEU* 3.1 8.4 + - - +
162P PRO* 1.3 72.5 - - - +
164P ALA* 1.3 66.5 + - - +
166P VAL* 3.3 2.3 + - - +
167P LEU* 3.0 36.6 + - + +
245P VAL* 5.9 1.6 - - + -
247P LEU* 4.2 17.7 - - + -
264P LEU* 4.4 5.8 - - + -
276P ILE* 4.3 8.5 - - + -
295P SER* 3.9 15.0 - - - +
297P VAL* 4.3 18.6 - - + -
312P VAL* 4.1 22.7 - - + -
314P ALA* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160P LEU* 2.8 18.3 + - + +
161P ALA* 3.6 8.3 - - - +
163P VAL* 1.3 78.4 - - - +
165P LYS* 1.3 58.8 + - - +
167P LEU* 3.9 5.2 - - - +
168P HIS* 2.8 34.0 + - - +
173P ILE* 4.3 4.7 - - + +
219P VAL* 4.5 2.7 - - + -
223P ILE* 4.4 1.1 - - - -
226P LEU* 4.0 19.3 - - + -
230P LEU* 4.5 15.5 - - + -
247P LEU* 4.6 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P GLY 4.2 17.3 - - - +
137P VAL* 4.0 28.5 - - + +
161P ALA 2.8 21.1 + - - +
162P PRO* 3.6 5.8 - - + +
163P VAL 3.2 0.2 - - - -
164P ALA* 1.3 74.0 - - - +
166P VAL* 1.3 58.4 + - + +
168P HIS* 3.8 3.2 - - - +
169P ASP* 2.8 60.4 + - - +
223P ILE* 3.7 19.5 - - + +
272P MET* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P PRO 3.2 13.8 + - - +
163P VAL 3.3 5.8 + - - +
165P LYS* 1.3 75.0 - - + +
167P LEU* 1.3 65.5 + - - +
169P ASP* 3.6 3.3 + - - -
170P ASN* 2.7 47.2 + - - +
263P VAL* 3.6 32.1 - - + +
264P LEU* 4.2 11.4 - - + -
267P ALA* 3.7 22.7 - - + -
271P THR* 5.2 2.2 - - - +
272P MET* 4.0 15.5 - - + -
276P ILE* 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P VAL* 3.0 24.4 + - + +
164P ALA 3.9 1.6 - - - +
166P VAL* 1.3 79.6 - - + +
168P HIS* 1.3 58.6 + - - +
170P ASN 3.3 0.2 + - - -
171P PHE* 2.8 51.0 + - + +
172P GLY 3.4 2.6 + - - -
173P ILE* 3.8 14.1 - - + +
247P LEU* 4.2 18.6 - - + -
249P VAL* 4.0 22.7 - - + -
251P VAL* 5.5 0.2 - - + -
260P VAL* 5.2 3.6 - - + -
263P VAL* 5.2 0.7 - - + -
264P LEU* 3.8 32.8 - - + -
310P VAL* 4.2 10.1 - - + -
312P VAL* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164P ALA 2.8 19.7 + - - +
165P LYS* 3.9 4.0 - - - +
167P LEU* 1.3 78.4 - - - +
169P ASP* 1.3 67.8 + - - +
172P GLY* 2.8 32.3 + - - +
173P ILE* 2.9 44.1 + - + +
223P ILE* 4.8 4.5 - - + -
225P GLU* 3.6 42.6 + - + +
226P LEU* 3.7 25.9 - - + +
229P LYS* 4.7 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165P LYS* 2.8 53.6 + - - +
166P VAL* 4.0 5.6 - - - +
168P HIS* 1.3 87.4 - - - +
170P ASN* 1.3 64.9 + - - +
225P GLU* 5.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166P VAL* 2.7 42.2 + - - +
168P HIS 3.2 0.2 - - - -
169P ASP* 1.3 85.7 - - - +
171P PHE* 1.3 83.2 + - + +
172P GLY 3.8 0.2 - - - -
253P LYS* 3.1 26.3 - - - +
263P VAL* 3.7 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167P LEU* 2.8 30.6 + - + +
170P ASN* 1.3 93.0 - - + +
172P GLY* 1.3 67.9 + - - +
251P VAL* 3.7 22.4 - - + -
252P GLU* 3.0 18.5 + - - +
253P LYS* 3.0 34.6 + - + +
254P PRO 5.3 0.4 - - - -
255P THR* 3.7 34.8 - - + -
259P GLN* 4.1 14.8 - - + -
260P VAL* 3.9 37.7 - - + -
263P VAL* 4.0 23.3 - - + -
310P VAL* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167P LEU 3.4 2.2 + - - -
168P HIS* 2.8 28.2 + - - -
171P PHE* 1.3 76.6 - - - +
173P ILE* 1.3 64.8 + - - -
251P VAL* 3.1 4.6 - - - -
252P GLU* 2.7 41.6 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il